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#2398 08/04/04 03:34 AM
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tribas Offline OP
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I have a question about when to specify NTRFRQ and when not to specify it. It's automatically set to 0 as the default unless specified. In my Periodic boundary condition with ewald summations, it says that I should specify a non-zero NTRFRQ and after reading, if IPRFRQ is less than NTRFRQ and it is not = to 0 it will result in errors because of negative square roots.

What are the reasons? What are some general guidlines to go by if using ewald summations or some other electrotatic calculation? Is there a big difference between the two, if specified or not in a md simulation?

Thanks so much for all of your help!

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I'm not sure about the square root error, but NTRFRQ should be set to
50 or 100 during a periodic boundary simulation. This stops the kinetic energy from redistributing from the atomic degress of freedom to rotational and translation degrees of the entire system. there is a paper by Cheatham from a few years ago that discusses this; i think the title contains the term "flying icecube" IPRFRQ is the print frequency. this should be equal to or a multiple of NTRFRQ.

alex


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rmv Online Content
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I think the "negative square root" comment in the documentation may no longer be true; there are certainly other such "legacy" comments in the .doc files, such as "SHAKE doesn't work with ABNR".

NTRFRQ could be a bit larger, such as 1000 or 5000 steps, but it does need to be done regularly for systems using Ewald and PBC.


Rick Venable
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Hello, everyone.

I have another question about this correction. The documentation defines NTRFRQ as "the step frequency for stopping the rotation and translation of the molecule during dynamics". Does anyone know if this refers to the centre of mass of the solute (protein) or of the whole system? If it is the entire system, would this still affect the motion of a protein fixed in space? The protein's CM does move during dynamics, but I'm wondering if this translation is being damped because of this correction.


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I see unrealistic energy drifts or Temperature dramatically drops at every NTRFRQ, then the thermostat brings it up to 298K quickly and the Temp still averages around the desired T.

If the same script run in serial, this does not happen.

I've tried using NTRFRQ of 500, 2000 and 5000 but it is still the same.

Here is number of steps vs Temp where NTRFRQ was 2000:
(This is a constant P simulation with PBC and Ewald)

DYNA> 0 101.82021
DYNA> 500 292.56681
DYNA> 1000 294.03164
DYNA> 1500 294.00821
DYNA> 2000 296.35426
DYNA> 2000 109.20435 **
DYNA> 2500 304.29684
DYNA> 3000 301.72762
DYNA> 3500 302.40833
DYNA> 4000 293.33502
DYNA> 4000 143.80550 **
DYNA> 4500 299.03628
DYNA> 5000 295.94476
DYNA> 5500 301.50405
DYNA> 6000 298.92981
DYNA> 6000 100.61126 **
DYNA> 6500 289.49014
DYNA> 7000 297.08095
DYNA> 7500 296.22182
DYNA> 8000 297.96478
DYNA> 8000 113.12729 **
DYNA> 8500 292.78126
DYNA> 9000 297.32491
DYNA> 9500 300.98892
DYNA> 10000 308.11360
DYNA> 10000 148.18669 **

Last edited by TGK; 10/14/09 09:29 PM.
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I've heard that AMBER does this on every time step, e.g. NTRFRQ 1, so you may wish to try smaller values. There's insufficient information to say anything more.


Rick Venable
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NTRFRQ should not influence the temperature of your system (at least not so much...). We have never seen any trace of the flying ice-cube in CHARMM simulations, so NTRFRQ is not very important, except perhaps in certain kinds of calculations (Ewald?).

I guess that the data you show are temperature vs number of steps. Is anything else happening (eg velocity rescaling) when the temperature is dropping?
It is strongly recommended to show actual (brief and relevant!) input/output rather than filtered (by your brains and fingers) descriptions.


Lennart Nilsson
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I've observed flying ice-cube kind of behavior when I used a large NTRFRQ (9999999.) When I visualize the trajectory, the whole system was clearly moving in one direction very fast.

Below, I copied part of the output (when the step # is 2000):

DYNA> 2000 4.00000 -9905.17912 2958.40203 -12863.58115 296.35426
DYNA PROP> 14.94794 -9890.35859 2997.09252 14.82054 3337.58775
DYNA INTERN> 204.79661 717.22765 64.93361 610.32137 25.25269
DYNA EXTERN> 852.71347 -9614.37106 0.00000 0.00000 0.00000
DYNA IMAGES> 56.81154 -1932.74044 0.00000 0.00000 0.00000
DYNA EWALD> 302.59179 -69467.71774 65316.59935 0.00000 0.00000
DYNA PRESS> 698.69788 -2923.75638 -997.19135 -1322.25605 48043.43578
DYNA XTLE> -11296.52102 -38.38690 -1392.92335 0.98646
---------- --------- --------- --------- --------- ---------
Crystal Parameters : Crystal Type = CUBI
DYNA A = 36.35337 B = 36.35337 C = 36.35337
DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
DYNA PIXX = -1017.75 PIYY = -1469.07 PIZZ = -1479.95
DYNA PIXY = 205.75 PIXZ = -397.14 PIYZ = -12.49
DYNA Gradient Norm = 57.65885

DYNAMC> Averages for the last 1000 steps:
AVER DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
AVER PROP: GRMS HFCTote HFCKe EHFCor VIRKe
AVER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
AVER EXTERN: VDWaals ELEC HBONds ASP USER
AVER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
AVER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
AVER PRESS: VIRE VIRI PRESSE PRESSI VOLUme
AVER XTLE: XTLTe SURFtension XTLPe XTLtemp
---------- --------- --------- --------- --------- ---------
AVER> 1000 4.00000 -9796.87462 2974.52000 -12771.39462 297.96886
AVER PROP> 14.52205 -9786.31053 3006.11897 10.56409 1703.69317
AVER INTERN> 185.33036 701.86591 61.27895 593.83122 22.07340
AVER EXTERN> 801.32138 -9517.84495 0.00000 0.00000 0.00000
AVER IMAGES> 23.92132 -1804.12633 0.00000 0.00000 0.00000
AVER EWALD> 311.73661 -69467.71774 65316.93525 0.00000 0.00000
AVER PRESS> 1809.68841 -2945.48385 -2574.27718 -1339.55537 48199.95369
AVER XTLE> -11290.20284 37.16098 -1493.85952 235.87371
---------- --------- --------- --------- --------- ---------
Lattice Parameters> Averages for the last 1000 steps:
Crystal Parameters : Crystal Type = CUBI
AVER A = 36.39275 B = 36.39275 C = 36.39275
AVER Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
AVER PIXX = -1315.35 PIYY = -1497.63 PIZZ = -1205.69
AVER PIXY = 22.29 PIXZ = -146.98 PIYZ = 111.00
AVER Gradient Norm = 149.28043

DYNAMC> RMS fluctuations for the last 1000 steps:
FLUC> 1000 4.00000 75.29710 39.24785 66.83405 3.93161
FLUC PROP> 0.27635 74.46436 39.46627 2.97416 1136.34768
FLUC INTERN> 16.01179 25.63727 4.91273 14.26394 2.88486
FLUC EXTERN> 54.64298 86.57928 0.00000 0.00000 0.00000
FLUC IMAGES> 21.26724 86.38090 0.00000 0.00000 0.00000
FLUC EWALD> 12.20004 0.00000 2.23563 0.00000 0.00000
FLUC PRESS> 719.52278 340.55916 1023.17832 480.95123 184.75409
FLUC XTLE> 4.80966 137.56791 72.25656 294.49733
---------- --------- --------- --------- --------- ---------
Lattice Parameters> RMS fluctuations for the last 1000 steps:
Crystal Parameters : Crystal Type = CUBI
FLUC A = 0.04647 B = 0.04647 C = 0.04647
FLUC Alpha = 0.00000 Beta = 0.00000 Gamma = 0.00000
FLUC PIXX = 656.92 PIYY = 672.43 PIZZ = 719.09
FLUC PIXY = 451.97 PIXZ = 418.12 PIYZ = 434.60
FLUC Gradient Norm = 59.04240

DYNAMC> Averages for the last 2000 steps:
LAVE> 2000 4.00000 -9693.71067 2976.04001 -12669.75069 298.12112
LAVE PROP> 14.09419 -9685.81878 3000.18814 7.89189 1580.57332
LAVE INTERN> 157.08264 656.49949 50.56237 603.77136 19.39429
LAVE EXTERN> 823.37438 -9605.17040 0.00000 0.00000 0.00000
LAVE IMAGES> 19.32879 -1595.91003 0.00000 0.00000 0.00000
LAVE EWALD> 351.54586 -69467.71774 65317.48829 0.00000 0.00000
LAVE PRESS> 1679.27943 -2732.99498 -2377.94707 -1038.62921 48446.45087
LAVE XTLE> -11282.93858 71.89055 -1608.88163 272.31065
---------- --------- --------- --------- --------- ---------
Lattice Parameters> Averages for the last 2000 steps:
Crystal Parameters : Crystal Type = CUBI
LAVE A = 36.45460 B = 36.45460 C = 36.45460
LAVE Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
LAVE PIXX = -1096.83 PIYY = -1386.95 PIZZ = -632.11
LAVE PIXY = -11.05 PIXZ = -199.44 PIYZ = 102.84
LAVE Gradient Norm = 141.26957

DYNAMC> RMS fluctuations for the last 2000 steps:
LFLC> 2000 4.00000 396.93309 318.58153 163.99348 31.91351
LFLC PROP> 0.49088 395.20239 317.10754 26.18522 1484.49453
LFLC INTERN> 35.87503 58.32175 13.37246 19.97723 4.62943
LFLC EXTERN> 95.74885 222.13388 0.00000 0.00000 0.00000
LFLC IMAGES> 25.34128 311.59437 0.00000 0.00000 0.00000
LFLC EWALD> 79.79414 0.00000 3.33438 0.00000 0.00000
LFLC PRESS> 848.55099 641.17183 1201.82729 1001.85183 286.66896
LFLC XTLE> 8.47327 1840.73640 434.40785 330.73002
---------- --------- --------- --------- --------- ---------
Lattice Parameters> RMS fluctuations for the last 2000 steps:
Crystal Parameters : Crystal Type = CUBI
LFLC A = 0.07195 B = 0.07195 C = 0.07195
LFLC Alpha = 0.00000 Beta = 0.00000 Gamma = 0.00000
LFLC PIXX = 1152.96 PIYY = 888.02 PIZZ = 1465.71
LFLC PIXY = 469.45 PIXZ = 421.80 PIYZ = 406.34
LFLC Gradient Norm = 63.44438

DRIFT/STEP (LAST-TOTAL): -0.16574614 -0.21970085
E AT STEP 0 : -9703.3546 -9466.0081
CORR. COEFFICIENT : -0.64254588 -0.32096043

DETAILS ABOUT CENTRE OF MASS
POSITION : -0.15254881 -0.10634869 0.40600406
VELOCITY : -6.02991621E-02 -2.16858513E-02 5.51894033E-02
ANGULAR MOMENTUM : 2970.2974 -102.76485 -3140.7645
KINETIC ENERGY : 97.719446
WRIDYN: RESTart file was written at step 2000
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
DYNA XTLE: XTLTe SURFtension XTLPe XTLtemp
---------- --------- --------- --------- --------- ---------
DYNA> 2000 4.00000 -11773.43187 1090.14928 -12863.58115 109.20435
DYNA PROP> 14.94794 -11062.84847 2160.61036 710.58340 107108.07683
DYNA INTERN> 204.79661 717.22765 64.93361 610.32137 25.25269
DYNA EXTERN> 852.71347 -9614.37106 0.00000 0.00000 0.00000
DYNA IMAGES> 56.81154 -1932.74044 0.00000 0.00000 0.00000
DYNA EWALD> 302.59179 -69467.71774 65316.59935 0.00000 0.00000
DYNA PRESS> 698.69788 -72104.08243 -997.19135-100852.18252 48043.43578
DYNA XTLE> -11296.52102 -38.38690 -1392.92335 0.98646
---------- --------- --------- --------- --------- ---------
Crystal Parameters : Crystal Type = CUBI
DYNA A = 36.35337 B = 36.35337 C = 36.35337
DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
DYNA PIXX = -8886.55 PIYY = -125674.97 PIZZ = -167995.03
DYNA PIXY = -30861.99 PIXZ = -135860.86 PIYZ = -151486.98
DYNA Gradient Norm = 57.65885

UPDECI: Image update at step 2011

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2011
UPDECI: Image update at step 2020

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2020
UPDECI: Image update at step 2030

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2030
UPDECI: Image update at step 2043

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2043
UPDECI: Image update at step 2054

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2054
UPDECI: Image update at step 2064

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2064
UPDECI: Image update at step 2074

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2074
UPDECI: Image update at step 2086

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2086
UPDECI: Image update at step 2099

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2099
DYNA> 2100 4.20000 -10637.40919 2791.01797 -13428.42716 279.58677
DYNA PROP> 14.95906 -10615.53614 2831.21105 21.87305 -566.30679
DYNA INTERN> 178.08940 655.48034 54.44868 581.49181 16.98408
DYNA EXTERN> 923.86509 -10247.48132 0.00000 0.00000 0.00000
DYNA IMAGES> 27.90640 -1749.33908 0.00000 0.00000 0.00000
DYNA EWALD> 280.71527 -69467.71774 65317.12992 0.00000 0.00000
DYNA PRESS> 2266.80582 -1889.26795 -3235.01560 -5.56800 48046.42460
DYNA XTLE> -12794.78841 158.28973 -2165.76781 33.91946
---------- --------- --------- --------- --------- ---------
Crystal Parameters : Crystal Type = CUBI

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Reduce NTRFRQ, esp. with Ewald; try 50 or 100


Rick Venable
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post your input, this is odd


Lennart Nilsson
Karolinska Institutet
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